A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-01-17, 02:40 UTC
based on data in:
/data/output/homology_networks/pggb_v1
ODGI
ODGI is an optimized dynamic graph/genome implementation, for efficient analysis and manipulation of pangenome graphs structured in the variation graph model.
Detailed ODGI stats table.
| Sample Name | Length | Nodes | Edges | Paths | Components | A | C | T | G | N |
|---|---|---|---|---|---|---|---|---|---|---|
| seqwish | 2206574 | 116710 | 163038 | 4016 | 595 | 770779 | 332110 | 772756 | 330888 | 19 |
| smooth | 2635922 | 136515 | 187517 | 4016 | 704 | 920651 | 417705 | 927539 | 369986 | 41 |
Sum of path node distances
For each path we iterate from node to node and count the node / nucleotide distance of nodes on the pangenome level normalized by the path length. If a node is reversed, we count the node distance twice.
This value allows you to evaluate the sorting goodness - how linear the graph is.
Mean links length
For each path we iterate from node to node and count the node / nucleotide distance mean_links_length
of nodes within the same path only. We then normalized by the path length.
This value allows you to evaluate the sorting goodness - how linear the graph is.